How to put all armature bones under 1 root bone
Select only top level bones.

Select only bones that have no parent, to be children of the new root bone. As can be seen in the picture fore_arm has been re-parented from presumably upper_arm to the root bone via incorrectly selecting all and parenting to new root.

Suggest, after adding new root bone (before any parenting), select all other bones on the same level, and parent those to new root.



For means of demonstration have added the rigify human rig and deleted the spine root bone, then added a new bone "Root".

Shift-select the bones in same level in outliner, lastly "Root" , parent CtrlP and choose either connected to have children connected to Root without offset, or, probably in most cases, offset.